nf-core/methylseq 4.1.0

• Highlights

  • Optional BWA-MEM2 support via --use_mem2 for BWA-Meth indexing and alignment
  • Nextflow requirement raised to 24.10.5
  • Broad module/template updates and CI hardening

• New

  • Add --use_mem2 to enable the BWA-MEM2 algorithm in BWA-Meth
    • BWA-Meth modules updated to honor use_mem2
    • fasta_index_bismark_bwameth subworkflow updated to pass use_mem2

• Improvements

  • Update template to nf-core/tools v3.3.2
  • General modules update
  • Add GitHub Actions CI for GPU test snapshot updates
  • Update AWS megatests workflow to use new CE org variables
  • Add Wave to ARM megatests

• Fixes

  • FastQC output added twice to multiqc_ch
  • Broken documentation links
  • Update BWA-Meth container to fix bwa-mem2 installation

• Testing

  • New test covering BWA-MEM2 indexing and alignment

• Requirements

  • Nextflow >=24.10.5

• Compatibility notes

  • Default behavior unchanged unless --use_mem2 is provided.

Full Changelog: 4.0.0...4.1.0

nf-core/methylseq v4.0.0 Release Notes

This release introduces major new features, significant refactoring, and extensive test suite improvements. Key highlights include the addition of a targeted sequencing analysis workflow, substantial refactoring of input handling and subworkflows for better modularity and robustness, and a complete overhaul of the testing framework.

Bug Fixes & Refactoring

• Core Refactoring (#539):
  • The FASTA index subworkflow was refactored to remove implicit parameter passing.
  • Fixed workflow versions collection and improved conditional logic for FastQC and MultiQC execution.
• Parabricks Fixes:
  • The minimum memory for PARABRICKS_FQ2BAMMETH has been increased to 100GB as suggested by the documentation (#528).
  • Fixed a parabricks/fq2bammeth failure on AWS Batch-like executors where symlinks don't exist (#536).
• General:
  • Reverted PR #523 which involved direct changes to subworkflows in the pipeline.
  • The pipeline template has been updated to nf-core/tools v3.2.0 (#504).
  • The pipeline template has been updated to nf-core/tools v3.3.1 (#504).

Pipeline Updates

• Targeted Sequencing (#516, #539):
  • A new --run_targeted_sequencing flag has been added to enable further analysis of targeted methylation experiments.
  • A new Targeted Sequencing subworkflow has been introduced with improved parameter handling and region-specific analysis capabilities.
  • The bedtools/intersect and picard/collecthsmetrics modules from nf-core/modules have been installed.
  • A new --collecthsmetrics parameter has been added to allow the collection of Picard HS metrics.
• Workflow & Parameter Changes:
  • Bwameth:
    • Added --all_contexts and --merge_context parameters (#516).
    • Removed the --comprehensive parameter (#516).
  • Bismark:
    • Decoupled --merge_non_CpG from --comprehensive in the Bismark workflow (#516).
  • Trimming:
    • Added a new skip_trimming_presets flag to overwrite any preset trimming options (#506).
    • Updated --pbat trimming options to 8|8|8|8 (#506).
    • Removed --cegx and --epignome preset trimming options as the kits are discontinued (#506).
  • GPU Usage:
    • Removed the --use_gpu parameter. Activating the gpu profile with --profile gpu is now the standard way to enable GPU-based pathways (#520).
  • Quality Control:
    • Added --skip_fastqc and --skip_multiqc parameters to allow skipping quality control steps (#539).

Testing Updates (#539)

• Test Suite Consolidation:
  • Removed 19 individual test files, replacing them with comprehensive test suites.
• New Test Suites:
  • bismark_variants.nf.test for comprehensive Bismark testing.
  • bismark_hisat_variants.nf.test for Bismark with HISAT2 aligner.
  • bwameth_variants.nf.test for comprehensive Bwameth testing.
  • targeted_sequencing_variants.nf.test for the new targeted sequencing workflow.
  • index_downloads.nf.test for testing index download scenarios.

What's Changed

• post release bump version by @sateeshperi in #497
• Update test command in usage.md by @fbnrst in #502
• Important! Template update for nf-core/tools v3.2.0 by @nf-core-bot in #504
• Update snapshot 3.2.0 template by @sateeshperi in #505
• create separate test_gpu profile by @sateeshperi in #517
• update ci runners to runson by @sateeshperi in #522
• Fix faix notprovided error by @lpantano in #523
• Added CUDA test for runsOn by @GallVp in #534
• Removed parameter use_gpu by @GallVp in #533
• Bumped PARABRICKS_FQ2BAMMETH memory to 100.GB by @GallVp in #535
• Revert fix faix error by @sateeshperi in #530
• Updated parabricks/fq2bammeth by @GallVp in #537
• skip trimming presets by @sateeshperi in #518
• Important! Template update for nf-core/tools v3.2.1 by @nf-core-bot in #525
• Targeted analysis by @dcarrillox in #516
• Important! Template update for nf-core/tools v3.3.1 by @nf-core-bot in #538
• refactor-workflow-tests by @sateeshperi in #539
• bump-version 4.0.0 by @sateeshperi in #540
• update metro map 4.0.0 by @sateeshperi in #542
• apply suggestions from code review by @sateeshperi in #543
• Dev -> Main v4.0.0 by @sateeshperi in #541

New Contributors

• @lpantano made their first contribution in #523
• @dcarrillox made their first contribution in #516

Full Changelog: 3.0.0...4.0.0

What's Changed

• post-release version bump by @sateeshperi in #450
• Fix/fasta gunzip & bismark align cache by @sateeshperi in #457
• Feat/fastq align dedup bismark by @sateeshperi in #465
• Fasta index bismark bwameth by @sateeshperi in #468
• Conf modules configs by @sateeshperi in #469
• run_preseq param + skip preseq/lcextrap by default by @sateeshperi in #470
• run_qualimap param and skip qualimap/bamqc by default by @sateeshperi in #471
• Removed ambiguity in the multilane sample information by @bounlu in #452
• Disable gunzip publish by @sateeshperi in #474
• CI: add gpu tag test job by @sateeshperi in #478
• Fasta align dedup bwameth by @sateeshperi in #475
• Checking if shards > 0 are present before firing tests by @GallVp in #484
• Updated metro maps. by @ewels in #479
• Test replicates by @sateeshperi in #486
• Doc updates by @sateeshperi in #489
• Template update for nf-core/tools v3.1.0 by @sateeshperi in #490
• Important! Template update for nf-core/tools v3.1.0 by @nf-core-bot in #488
• 2.8.0 bump-version by @sateeshperi in #491
• Cytosine report test by @sateeshperi in #493
• First attempt at fact-checking chatGPT by @FelixKrueger in #495
• add bs-seq-primer doc by @sateeshperi in #494
• bump ver to 3.0.0 semver by @sateeshperi in #496
• Dev -> Master 3.0.0 by @sateeshperi in #492

New Contributors

• @bounlu made their first contribution in #452
• @GallVp made their first contribution in #484

Full Changelog: 2.7.1...v3.0.0

What's Changed

• post-release version bump by @sateeshperi in #446
• Patch release 2.7.1 by @sateeshperi in #448
• Dev -> Master 2.7.1 by @sateeshperi in #449

Full Changelog: 2.7.0...2.7.1

What's Changed

• post-release dev bump version and snapshots by @sateeshperi in #371
• add missing comma to awstestfull yml by @sateeshperi in #375
• Important! Template update for nf-core/tools v2.12 by @nf-core-bot in #377
• Fix/samplename join by @sateeshperi in #381
• Important! Template update for nf-core/tools v2.13 by @nf-core-bot in #380
• Important! Template update for nf-core/tools v2.13.1 by @nf-core-bot in #384
• remove duplicate section from usage.md by @fbnrst in #386
• Important! Template update for nf-core/tools v2.14.1 by @nf-core-bot in #399
• Fix/sample merge by @sateeshperi in #401
• test(#392): Add boilerplate for tests by @edmundmiller in #393
• fix usage of Fasta references for bwameth / samtools faidx by @maxulysse in #403
• Bump preseq by @ewels in #390
• Add length_trim parameter to nextflow.config file by @geethavenk in #416
• Add missing type field to entry in nextflow_schema.json by @scoughlan2 in #417
• Feat/workflow updates by @sateeshperi in #414
• Fix/readme 391 by @sateeshperi in #418
• bump-version and update CHANGELOG by @sateeshperi in #419
• update date for 2.7.0 release by @sateeshperi in #421
• Template update for nf-core/tools v3.0.2 by @sateeshperi in #426
• Important! Template update for nf-core/tools v3.0.2 by @nf-core-bot in #427
• update bismark+bwameth modules; sub-wf; wf by @sateeshperi in #428
• udpate tests to use nft-bam for bam files by @sateeshperi in #429
• update SAMTOOLS_FAIDX fasta input after reorg by @sateeshperi in #430
• apply code review suggestions and activate igenomes bwameth index use by @sateeshperi in #431
• @sateeshperi fix bismark, bwameth align modules * other module updates + update snaps by @sateeshperi in #432
• update CI and Changelog by @sateeshperi in #433
• update spacing in nextflow.config to test nf-test trigger by @sateeshperi in #434
• rm conda from CI tests until the file lock resolution by @sateeshperi in #435
• Adding Metromap (with Sections) by @Shaun-Regenbaum in #438
• rm resourceLimits for test_full profile by @sateeshperi in #439
• update changelog and readme by @sateeshperi in #442
• Update metromap.svg by @ewels in #443
• add hisat2 bismark index to igenomes by @sateeshperi in #444
• apply suggestions from nextflow vscode formatter + update date in cha… by @sateeshperi in #445
• Dev -> Master 2.7.0 by @sateeshperi in #420

New Contributors

• @fbnrst made their first contribution in #386
• @geethavenk made their first contribution in #416
• @scoughlan2 made their first contribution in #417
• @Shaun-Regenbaum made their first contribution in #438

Full Changelog: 2.6.0...2.7.0

Pipeline Updates

• 🔄 Updated template to nf-core/tools v2.11.1 #368 @sateeshperi @edmundmiller

Bug fixes & refactoring

• 🛠 Copy methylKit-compatible files to publishDir #357 @ltosti-tagomics
• 🐛 fix ignore_r1 and ignore_3prime_r1 variable expansion #359 @noecochetel
• 🐛 No groups #362 @edmundmiller

Pipeline Updates

• 🔄 Updated template to nf-core/tools v2.9
• 🔄 Updated template to nf-core/tools v2.10
• 🔧 Updated nf-core modules for FastQC, samtools sort, samtools flagstat @ewels
  • ❌ Removes problematic -m memory assignment for samtools sort #81
• 🧾 Use fromSamplesheet from nf-validation #341 @emiller88
• 🚀 Update Maintainers and add CODEOWNERS #345 @emiller88
• ⚙️ Update schema to utilize exists and add more patterns #342 @emiller88
• 📁 Support pipeline-specific configs #343 @maxulysse

Bug fixes & refactoring

• 🛠️ Added publishing of coverage (*cov.gz) files for NOMe-seq filtered reads for coverage2cytosine @FelixKrueger
• 🛠️ Wrong display values for "zymo" and "em_seq" presets on help page #335 @wassimsalam01
• 📚 Use new Citation tools functions #336 @emiller88

Full Changelog: 2.4.0...2.5.0

Pipeline Updates

• Updated template to nf-core/tools v2.8
• Add --bamqc_regions_file parameter for targeted methylation sequencing data #302
• ✨ Add NF-TEST tests and snapshots for the pipeline test profile #310

Bug fixes & refactoring

• 🛠️ update index file channels to explicit value channels #310
• 🐛 fix params.test_data_base in test and test_full configs #310
• 🤖 GitHub Actions CI - pull_reqest to dev tests with NXF_VER latest-everything #310
• 🤖 GitHub Actions CI - pull_reqest to master tests with NXF_VER 22.10.1 & latest-everything #310
• 🤖 GitHub Actions CI - fail-fast set to false #310
• 🐛 get to the bottom of index tests #278
• ✨ Support for Bismark methylation extraction ignore and ignore_3prime parameters when ignore_r1 or ignore_3prime_r1 are greater than 0. #322
• 🛠️ rename ignore -> ignore_r1 and ignore_3prime -> ignore_3prime_r1 params #322
• 🐛 removed unused directory #297

Pipeline Updates

• ⚙️ Dramatically increase the default process time config requests for Bismark and bwa meth alignment
• ✨ Add a tower.yml file to enable Reports in Nextflow Tower
• 🤖 GitHub Actions CI - download the test data prior to running tests

Bug fixes & refactoring

• 🧹 Refactor genome indices preparation into a separate workflow
• 🧹 Refactor subworkflow logic out of alignment subworkflows, for later sharing
• 🐛 Fix a bug with using a local genome reference FASTA file
• 🐛 Fix a bunch of problems in the CI tests using nf-test (#279)

Pipeline Updates

• ✨ Updated the bismark2summary step so that it no longer stages the aligned BAM files into the working directory (#268)
  • Should be much faster / cheaper for running on the cloud
• ✨ Added ability to merge FastQ files based on shared IDs in sample sheet (#272)

Bug fixes & refactoring

• 🐛 Fixed typo in parameter handling for input reference indices (#263)
• 🧹 Removed orphaned --bismark_align_cpu_per_multicore and --bismark_align_cpu_per_multicore parameters.
  • Multi-core usage for Bismark alignment is now automatically set. If you would like to overwrite this, you can do so by setting ext.args for the process in a custom config.
• 🧹 Removed duplicate option --coverage2cytosine (#273)
  • Use the existing option --cytosine_report to launch the new COVERAGE2CYTOSINE process.
  • Removed option --cytosine_report genome_index from the Bismark methylation extractor.